Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,231,143 |
C→G |
P878A (CCC→GCC) |
glnE → |
glutamine synthetase adenylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,231,143 | 0 | C | G | 100.0%
| 42.4
/ NA
| 13 | P878A (CCC→GCC) | glnE | glutamine synthetase adenylyltransferase |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (6/7); total (6/7) |
GCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCC > AM260479/1231027‑1231253
|
gccgcAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCt > 2:563666/1‑133 (MQ=255)
aaGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGCgggc < 1:360236/134‑2 (MQ=255)
gCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGCgggcaat < 1:902866/134‑5 (MQ=255)
accgaccTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTgcg < 1:563666/134‑1 (MQ=255)
aGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGgcgc < 1:578359/72‑1 (MQ=255)
aGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGgcgc > 2:578359/1‑72 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCgctgc > 1:268559/1‑72 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCgctgc < 2:268559/72‑1 (MQ=255)
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGcc > 1:619302/1‑134 (MQ=255)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAatat < 1:530887/50‑1 (MQ=25)
ctgctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAatat > 2:530887/1‑50 (MQ=25)
gctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCa < 1:915744/35‑1 (MQ=25)
gctgcAC‑AGCCGGGCGCACCCGCAGCTGACGCGCa > 2:915744/1‑35 (MQ=25)
|
GCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCC > AM260479/1231027‑1231253
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCT > AM260479/1231015‑1231254
|
cgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGC < GWNJ‑0478:712:GW2002102894th:2:2104:19621:24881/103‑1 (MQ=60)
cattgtttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCG < GWNJ‑0478:712:GW2002102894th:2:2211:2292:31919/65‑1 (MQ=60)
GAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTG < GWNJ‑0478:712:GW2002102894th:2:1208:15380:3127/150‑1 (MQ=60)
GGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGC < GWNJ‑0478:712:GW2002102894th:2:2208:10703:52623/150‑1 (MQ=60)
tttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGC < GWNJ‑0478:712:GW2002102894th:2:2101:8238:87333/81‑1 (MQ=60)
GACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCT < GWNJ‑0478:712:GW2002102894th:2:2105:6258:24490/150‑1 (MQ=60)
gtataagagacaGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGG < GWNJ‑0478:712:GW2002102894th:2:1113:4232:59011/137‑1 (MQ=60)
GTCGATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTG < GWNJ‑0478:712:GW2002102894th:2:1116:10293:5639/63‑1 (MQ=60)
ATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGctgtctcttatacacatctccgagcccacgagacggagctacatctcg > GWNJ‑0478:712:GW2002102894th:2:1201:12669:94484/1‑102 (MQ=60)
ATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCT > GWNJ‑0478:712:GW2002102894th:2:2106:12577:95196/1‑150 (MQ=60)
|
TCATGCAGATGCGCCGCAAGGTCGCCGAAGGCCATCCCAACCCGACCGACCTGTTCGACCTGAAGCACGATCGCGGCGGCATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCT > AM260479/1231015‑1231254
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
